This paper addresses a mathematical model and dynamic analysis of multi-unit hydropower systems in transient process. In this work, the first unit is assumed to be subject to a sudden load decrease, while the second unit runs with load. A approach to the description of the six stochastic dynamic transfer coefficients of the hydro-turbine is proposed for the second unit. Moreover, a novel dynamic model for the multi-unit hydropower system, able to take into account the eventual occurrence of water hammer in the penstock and the nonlinearity of the generator, is introduced. Also, a numerical application is analyzed in order to investigate the effectiveness of the approach proposed and the dynamic characteristics of the system under study. Finally, a comparative analysis is proposed in order to validate the proposed system. The methods and results implemented in this work provide theoretical tools to guarantee the stable operation of hydropower stations.